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make_bids.sh
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# from dicom to bids, includes defacing with mri_deface
tag="movie_fMRI"
NS=3;
subprefix=""
Nruns=3;
declare -a subjIDs=("3595" "3612" "3880");
declare -a tasks=( "rest" "movie" "rest")
anat_id='00005';
declare -a funct_id=("00002" "00003" "00004")
basepath='./braindata/eglerean/PAS/';
i=1;
for s in ${subjIDs[@]}; do
## sub-<participant_label>[_acq-<label>][_rec-<label>][_run-<index>]_T1w.nii.gz
echo mkdir -p $basepath/$tag/sub-$subprefix$i/anat
mkdir -p $basepath/$tag/sub-$subprefix$i/anat
echo "###" Creating file $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w_nodeface.nii"
echo "###" Creating file $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w.json"
echo dcm2niix -b y -o $basepath/$tag/sub-$subprefix$i/anat -f sub-$subprefix$i"_T1w_nodeface" $basepath/$s/$s/$anat_id
dcm2niix -b y -o $basepath/$tag/sub-$subprefix$i/anat -f sub-$subprefix$i"_T1w_nodeface" $basepath/$s/$s/$anat_id
echo mv $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w_nodeface.json $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w.json
echo "### Defacing: " $basepath/bin/mri_deface $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w_nodeface.nii" $basepath/bin/talairach_mixed_with_skull.gca $basepath/bin/face.gca $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w.nii"
$basepath/bin/mri_deface $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w_nodeface.nii" $basepath/bin/talairach_mixed_with_skull.gca $basepath/bin/face.gca $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w.nii"
echo rm $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w_nodeface.nii"
rm $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w_nodeface.nii"
echo gzip $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w.nii"
gzip $basepath/$tag/sub-$subprefix$i/anat/sub-$subprefix$i"_T1w.nii"
## sub-<participant_label>/func/sub-<participant_label>_task-<task_label>[_acq-<label>][_run-<index>]_bold.json
echo mkdir -p $basepath/$tag/sub-$subprefix$i/func
mkdir -p $basepath/$tag/sub-$subprefix$i/func
let lim=$Nruns-1;
for r in $(seq 0 $lim); do
let rr=$r+1;
echo "### Creating " $basepath/$tag/sub-$subprefix$i/func/sub-$subprefix$i"_task-"${tasks[$r]}"_acq-EPI_run-"$rr"_bold"
echo dcm2niix -b y -o $basepath/$tag/sub-$subprefix$i/func -f sub-$subprefix$i"_task-"${tasks[$r]}"_acq-EPI_run-"$rr"_bold" $basepath/$s/$s/${funct_id[$r]}
dcm2niix -b y -o $basepath/$tag/sub-$subprefix$i/func -f sub-$subprefix$i"_task-"${tasks[$r]}"_acq-EPI_run-"$rr"_bold" $basepath/$s/$s/${funct_id[$r]}
if [ $r -eq 1 ]; then
cp $basepath/$s/$s.log $basepath/$tag/sub-$subprefix$i/func/sub-$subprefix$i"_task-"${tasks[$r]}"_acq-EPI_run-"$rr"_events.tsv"
fi
done
let i=$i+1;
done
# extra folders for data perservation
mkdir ./braindata/eglerean/PAS/movie_fMRI/permissions
mkdir ./braindata/eglerean/PAS/movie_fMRI/stimuli
mkdir ./braindata/eglerean/PAS/movie_fMRI/experiments